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A phytochemical study on the stems and leaves of Cratoxylum cochinchinense (Lour.) Blume resulted in the isolation and characterisation of a new polyprenylated xanthone, cratocochinone (1), as well as seven known analogues, fuscaxanthone K (2), pruniflorone Q (3), 1,3,5,8-tetrahy-droxy- 2-(3-methybut-2-enyl)-4-(3,7-dimethylocta-2,6-dienyl) xanthone (4), cochinensoxanthone (5), cratoxylum-xanthone B (6), cochinchinone I (7) and cochinchinone K (8). The chemical structure of 1 was determined by comprehensive spectral analyses. The known compounds 2 - 8 were identified by comparing their experimental spectroscopic data with those reported data in the literature. The anti-inflammatory and anti-HIV effects of all isolates 1-8 were evaluated. As a result, compounds 1-8 showed remarkable inhibitory effects against nitric oxide (NO) production induced by lipopolysaccharide in mouse macrophage RAW 264.7 cells showing IC50 values ranging from 0.68 ± 0.06 to 10.27 ± 0.18 µM. Meanwhile, compounds 1-8 displayed notable anti-HIV-1 reverse transcriptase (RT) effects with EC50 values ranging from 0.19 to 10.72 µM.

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One of the main challenges in co-injection molding is how to predict the skin to core morphology accurately and then manage it properly, especially after skin material has been broken through. In this study, the formation of the Core-Skin-Core (CSC) structure and its physical mechanism in a two-stage co-injection molding has been studied based on the ASTM D638 TYPE V system by using both numerical simulation and experimental observation. Results showed that when the skin to core ratio is selected properly (say 30/70), the CSC structure can be observed clearly at central location for 30SFPP/30SFPP system. When the skin to core ratio and operation conditions are fixed, regardless of material arrangement (including 30SFPP/30SFPP; PP/PP; 30SFPP/PP; and PP/30SFPP systems), the morphologies of the CSC structures are very close for all systems. This CSC structure can be further validated by using µ-CT scan and image analysis technologies perfectly. Furthermore, the influences of various operation parameters on the CSC structure variation have been investigated. Results exhibited that the CSC structure does not change significantly irrespective of the flow rate changing, melt temperature varying, or even mold temperature being modified. Moreover, the mechanism to generate the CSC structure can be derived using the melt front movement of the numerical simulation. It is worth noting that after the skin material was broken through, the core material travelled ahead with fountain flow to occupy the flow front. In the same period, the proper amount of skin material with certain inertia of enough kinetic energy will keep going to penetrate the new coming core material to travel until the end of filling. It ends up with this special CSC structure.

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Transition metal phosphorus trisulfide materials have received considerable research interest since the 1980-1990s as they exhibit promising energy conversion and storage properties. However, the mechanistic insights into Li-ion storage in these materials are poorly understood to date. Here, we explore the lithiation of NiPS3 material by employing in situ pair-distribution function analysis, Monte Carlo molecular dynamics calculations, and a series of ex situ characterizations. Our findings elucidate complex ion insertion and storage dynamics around a layered polyanionic compound, which undergoes intercalation and conversion reactions in a sequential manner. This study of NiPS3 material exemplifies the Li-ion storage mechanism in transition metal phosphorus sulfide materials and provides insights into the challenges associated with achieving reliable, high-energy phosphorus trisulfide systems.

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Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear. Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail. Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

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Catastrophic accidents caused by fatigue failures often occur in engineering structures. Thus, a fundamental understanding of cyclic-deformation and fatigue-failure mechanisms is critical for the development of fatigue-resistant structural materials. Here we report a high-entropy alloy with enhanced fatigue life by ductile-transformable multicomponent B2 precipitates. Its cyclic-deformation mechanisms are revealed by real-time in-situ neutron diffraction, transmission-electron microscopy, crystal-plasticity modeling, and Monte-Carlo simulations. Multiple cyclic-deformation mechanisms, including dislocation slips, precipitation strengthening, deformation twinning, and reversible martensitic phase transformation, are observed in the studied high-entropy alloy. Its improved fatigue performance at low strain amplitudes, i.e., the high fatigue-crack-initiation resistance, is attributed to the high elasticity, plastic deformability, and martensitic transformation of the B2-strengthening phase. This study shows that fatigue-resistant alloys can be developed by incorporating strengthening ductile-transformable multicomponent intermetallic phases.

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The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and non-amniote vertebrates. Here, we carried out a systematic study of the relationship between 5' UTR length and gene expression pattern in the chicken genome. We found that gene 5' UTRs lengths show a negative correlation with gene expression levels and gene expression breadths significantly. The relevance of 5' UTR length to expression pattern can not be a consequence of transcription-associated mutations. We also found that gene 5' UTR length shows a weakly positive correlation with gene tissue specificity. Another intriguing finding is that genes with 5' UTR length <30 bp have highest expression level, highest expression breadth, and lowest tissue specificity in chicken. We argued that selection is likely involved in shaping 5' UTR length in the chicken genome.

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BACKGROUND: GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution. METHODS: Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5' untranslated region sequences (5' UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1. RESULTS: In chicken, the GC content of 5' UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression. CONCLUSIONS: GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.

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Insertions and deletions (Indel) are important sources of genetic diversity and phenotypic divergence. Many factors such as mutation, recombination, selection and genetic drift can jointly affect the indel distribution across the genome. Studies of the relationship between recombination and indel density can, to a certain extent, reflect the selective constrain on indel. Based on the improved genetic map, genome sequence assembly and the partial (0.25X) shotgun sequencing of three breeds of domestic chicken, we calculated the recombination rates and the indel density segregating within introns and intergenic for 4 Mb windows (n = 210). Regression analyses demonstrated that recombination rates are significantly correlated with intron indel density, but not with the intergenic indel density. After adjusted regional effect, the significant trend was remained. This implies that selection is an important factor to influence the indel distribution within introns in chicken genome. By contrast, the intergenic indel seem to be neutral. Since the intron indel density on Z chromosome is less than half of that on autosomes, we preliminarily deduced that genetic hitchhiking might be more important than background selection in producing the observed correlation. As these two processes are not mutually exclusive, it is most likely that both contribute somewhat to the observed pattern. In result similar to previous study, we also found SNP density is highly correlated with indel density. Based on this characteristic, a hypothesis suggested that there are common effects of mutation and/or selection on the occurrence of indel and point mutations. This hypothesis can not explain our observations.

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BACKGROUND: Coding sequence (CDS) length, gene size, and intron length vary within a genome and among genomes. Previous studies in diverse organisms, including human, D. Melanogaster, C. elegans, S. cerevisiae, and Arabidopsis thaliana, indicated that there are negative relationships between expression level and gene size, CDS length as well as intron length. Different models such as selection for economy model, genomic design model, and mutational bias hypotheses have been proposed to explain such observation. The debate of which model is a superior one to explain the observation has not been settled down. The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. As D. Melanogaster, chicken has a larger effective population size, selection for chicken genome is expected to be more effective in increasing protein synthesis efficiency. Therefore, in this study the chicken was used as a model organism to elucidate the interaction between gene features and expression pattern upon selection pressure. RESULTS: Based on different technologies, we gathered expression data for nuclear protein coding, single-splicing genes from Gallus gallus genome and compared them with gene parameters. We found that gene size, CDS length, first intron length, average intron length, and total intron length are negatively correlated with expression level and expression breadth significantly. The tissue specificity is positively correlated with the first intron length but negatively correlated with the average intron length, and not correlated with the CDS length and protein domain numbers. Comparison analyses showed that ubiquitously expressed genes and narrowly expressed genes with the similar expression levels do not differ in compactness. Our data provided evidence that the genomic design model can not, at least in part, explain our observations. We grouped all somatic-tissue-specific genes (n = 1105), and compared the first intron length and the average intron length between highly expressed genes (top 5% expressed genes) and weakly expressed genes (bottom 5% expressed genes). We found that the first intron length and the average intron length in highly expressed genes are not different from that in weakly expressed genes. We also made a comparison between ubiquitously expressed genes and narrowly expressed somatic genes with similar expression levels. Our data demonstrated that ubiquitously expressed genes are less compact than narrowly expressed genes with the similar expression levels. Obviously, these observations can not be explained by mutational bias hypotheses either. We also found that the significant trend between genes' compactness and expression level could not be affected by local mutational biases. We argued that the selection of economy model is most likely one to explain the relationship between gene expression and gene characteristics in chicken genome. CONCLUSION: Natural selection appears to favor the compactness of highly expressed genes in chicken genome. This observation can be explained by the selection of economy model.

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Linkage disequilibrium (LD) analyses play a fundamental role in gene mapping, both as a tool for fine mapping of complex trait gene and in genome-wide association studies. The use of LD analyses in practice depends crucially on the understanding of the patterns of LD in the genome. In the present study, a total of 36 SNP were selected initially in a region (200 kb) of Contig.060226.1 on GGA1 based on the average physical distance. After verifying their level of polymorphism, 21 SNP were selected finally to genotype one wild and two domestic chicken populations, Red Jungle Fowl (RJF), Taihe Silkie chicken (TS) and White Recessive Rock chicken (WRR). Two distinct measures of linkage disequilibrium, D' and r(2), between marker pairs were used. The D'map of RJF is spurious. Many marker pairs showed complete LD. TS and WRR showed distinct characteristic of decreasing D' value over increasing physical distance. The r(2) showed much less inflation than did D' in RJF population, and also showed a characteristic decreasing value over increasing physical distance. In TS and WRR populations, although the two measures differed in scale, their decay profiles were similar. The data in the present study suggested that the extent of LD in this region is about 150 kb, corresponding to 0.4 cM. Our results imply that a very dense map of SNP markers will be required for LD mapping methods. Thus, association studies based on polymorphisms within all known genes, and candidate QTL mapping, may ultimately prove to be a more effective strategy.

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Three new polyphenols, araspidin BB (1), arachniodesin A (2) and arachniodesin B (3), together with two known compounds, epicatechin (4) and procyanidin B-2 (5), were isolated from the rhizomes of Arachniodes exilis. The structures of three new compounds were elucidated as 5-methyl-methylene-bis-phlorobutyrophenone (1), 4beta-ethoxycarbonylmethylepicatechin (2) and epicatechin-(4beta --> 8)-4beta-ethoxycarbonylmethylepicatechin (3), on the basis of their spectral analysis and by comparing them with the related model compounds. Compounds 4 and 5 were obtained from the title plant for the first time.

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A region (200 kb) of Contig. 060226.1 on GGA1 was selected to study the average diversity of Red Jungle Fowl (RJF), Taihe Silk chicken (TS), and White Recessive Rock (WRR), and estimate the effective population size (Ne) of chicken. The mean heterozygosities of RJF, TS and WRR were 0.28533+/-0.034747, 0.32926+/-0.039191 and 0.30168+/-0.040382, respectively. Significant test indicted that there is not significant difference between them (P=0.2368>0.05). The initial chicken effective population size was estimated to be about 20 000-150 000. Chicken has undergone serious population bottleneck effect during the first stage of domestication. However, this bottleneck effect did not result in a substantial loss of diversity as revealed by SNP. The possible explanations for similar SNP diversity between domesticated chicken and Red Jungle Fowl might due to many factors, such as a big Ne in earlier phase of domestication, population expending in breed differentiation, abroad crossing between breeds (especially crossing with RJF), together with high recombination rate in chicken genome.

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As an important economically animal and a model animal, a great of progress of SNP diversity and QTL mapping in chickens have been made in recent years. The present paper not only summarized these achievements but also commanded an extensive view about the fine mapping of QTL by the use of SNP marker.

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